Abstract：
:Functional genomics data has the potential to increase GWAS power by identifying SNPs that have a higher prior probability of association. Here, we introduce a method that leverages polygenic functional enrichment to incorporate coding, conserved, regulatory, and LD-related genomic annotations into association analyses. We show via simulations with real genotypes that the method, functionally informed novel discovery of risk loci (FINDOR), correctly controls the false-positive rate at null loci and attains a 9%-38% increase in the number of independent associations detected at causal loci, depending on trait polygenicity and sample size. We applied FINDOR to 27 independent complex traits and diseases from the interim UK Biobank release (average N = 130K). Averaged across traits, we attained a 13% increase in genome-wide significant loci detected (including a 20% increase for disease traits) compared to unweighted raw p values that do not use functional data. We replicated the additional loci in independent UK Biobank and non-UK Biobank data, yielding a highly statistically significant replication slope (0.66-0.69) in each case. Finally, we applied FINDOR to the full UK Biobank release (average N = 416K), attaining smaller relative improvements (consistent with simulations) but larger absolute improvements, detecting an additional 583 GWAS loci. In conclusion, leveraging functional enrichment using our method robustly increases GWAS power.
journal_name
Am J Hum Genetjournal_title
American journal of human geneticsauthors
Kichaev G,Bhatia G,Loh PR,Gazal S,Burch K,Freund MK,Schoech A,Pasaniuc B,Price ALdoi
10.1016/j.ajhg.2018.11.008subject
Has Abstractpub_date
2019-01-03 00:00:00pages
65-75issue
1eissn
0002-9297issn
1537-6605pii
S0002-9297(18)30411-7journal_volume
104pub_type
杂志文章abstract：:The poly(ADP-ribose) polymerase (PADPRP) gene (13q33-qter) depicts a two-allele (A/B) polymorphism. In the noncancer population, the frequency of the B allele is higher among blacks than among whites. Since the incidence of multiple myeloma and prostate and lung cancer is higher in the U.S. black population, we have a...
journal_title：American journal of human genetics
pub_type： 杂志文章
doi：
更新日期：1993-01-01 00:00:00
abstract：:One widely used measure of genetic similarity for pairs of relatives is gene identity-by-descent (IBD) sharing. Genes that are copies of a single gene in a common ancestor of the individuals who now carry them are said to be IBD. One obvious extension of the IBD concept is IBD gene(s) shared by more than two individua...
journal_title：American journal of human genetics
pub_type： 杂志文章
doi：
更新日期：1995-06-01 00:00:00
abstract：:We describe a log-linear method for analysis of case-parent-triad data, based on maximum likelihood with stratification on parental mating type. The method leads to estimates of association parameters, such as relative risks, for a single allele, and also to likelihood ratio chi2 tests (LRTs) of linkage disequilibrium...
journal_title：American journal of human genetics
pub_type： 杂志文章
doi：10.1086/301802
更新日期：1998-04-01 00:00:00
abstract：:The reported linkage between cutaneous melanoma and the dysplastic nevus syndrome (CM/DNS) to markers located on the distal portion of the short arm of chromosome 1 was examined in three Utah kindreds ascertained for multiple cases of melanoma. Family members in these kindreds were genotyped for the two markers report...
journal_title：American journal of human genetics
pub_type： 杂志文章
doi：
更新日期：1990-05-01 00:00:00
abstract：:Protoporphyria is an autosomal dominant disease in man in which protoporphyrin accumulated because of a defect in heme synthase (ferrochelatase) activity. A disease has been described in cattle that has the same manifestations as does the human disease. We measured heme synthase activity in sonicates of cultured skin ...
journal_title：American journal of human genetics
pub_type： 杂志文章
doi：
更新日期：1982-03-01 00:00:00
abstract：:Bloom syndrome (BS) is an autosomal recessive disorder characterized by increases in the frequency of sister-chromatid exchange and in the incidence of malignancy. Chromosome-transfer studies have shown the BS locus to map to chromosome 15q. This report describes a subject with features of both BS and Prader-Willi syn...
journal_title：American journal of human genetics
pub_type： 杂志文章
doi：
更新日期：1994-07-01 00:00:00
abstract：:gamma-Aminobutyric acid transaminase (GABAT, E.C.2.6.I.19) was phenotyped by starch-gel electrophoresis in post-mortem liver samples from 650 unrelated subjects of either sex, comprising 289 Chinese, 177 Indians, 140 Malays, and 44 from other racial groups from Southeast Asia. The estimated gene frequencies of GABAT1 ...
journal_title：American journal of human genetics
pub_type： 杂志文章
doi：
更新日期：1985-03-01 00:00:00
abstract：:Myotubular myopathy is a severe congenital disease inherited as an X-linked trait (MTM1; McKusick 31040). It has been mapped to the long arm of chromosome X, to the Xq27-28 region. Significant linkage has subsequently been established for the linkage group comprised of DXS304, DXS15, DXS52, and F8C in several studies....
journal_title：American journal of human genetics
pub_type： 杂志文章
doi：
更新日期：1995-07-01 00:00:00
abstract：:To test hypotheses about the origin of modern humans, we analyzed mtDNA sequences, 30 nuclear restriction-site polymorphisms (RSPs), and 30 tetranucleotide short tandem repeat (STR) polymorphisms in 243 Africans, Asians, and Europeans. An evolutionary tree based on mtDNA displays deep African branches, indicating grea...
journal_title：American journal of human genetics
pub_type： 杂志文章
doi：10.1002/ajmg.1320570340
更新日期：1995-09-01 00:00:00
abstract：:When the mode of inheritance of a disease is unknown, the LOD-score method of linkage analysis must take into account uncertainties in model parameters. We have previously proposed a parametric linkage test called "MFLOD," which does not require specification of disease model parameters. In the present study, we intro...
journal_title：American journal of human genetics
pub_type： 杂志文章
doi：10.1086/302888
更新日期：2000-05-01 00:00:00
abstract：:Although balanced translocations are among the most common human chromosomal aberrations, the constitutional t(11;22)(q23;q11) is the only known recurrent non-Robertsonian translocation. Evidence indicates that de novo formation of the t(11;22) occurs during meiosis. To test the hypothesis that spatial proximity of ch...
journal_title：American journal of human genetics
pub_type： 杂志文章
doi：10.1086/507652
更新日期：2006-09-01 00:00:00
abstract：:Congenital limb malformations rank behind only congenital heart disease as the most common birth defects observed in infants. Finding genes that cause defects in human limb patterning should be straightforward but has been limited, in part, by the bewildering spectrum of phenotypes, which are difficult to separate int...
journal_title：American journal of human genetics
pub_type： 杂志文章
doi：10.1086/301687
更新日期：1998-01-01 00:00:00
abstract：:The segregation of COL1A1 and COL1A2, the two genes which encode the chains of type I collagen, was analyzed in 38 dominant osteogenesis imperfecta (OI) pedigrees by using polymorphic markers within or close to the genes. This was done in order to estimate the consistency of linkage of OI genes to these two loci. None...
journal_title：American journal of human genetics
pub_type： 杂志文章
doi：
更新日期：1990-02-01 00:00:00
abstract：:In a study of 908 males from Europe, northern Africa, and western Asia, the variation of four Y-linked dinucleotide microsatellites was analyzed within three "frames" that are defined by mutations that are nonrecurrent, or nearly so. The rapid generation and extinction of new dinucleotide length variants causes the ha...
journal_title：American journal of human genetics
pub_type： 杂志文章,多中心研究
doi：10.1086/301999
更新日期：1998-09-01 00:00:00
abstract：:When population geneticists wish to determine the genetic consequences of some aspect of mating behavior, it is often necessary to compare observed levels of consanguinity to the level expected when mating is random with respect to the factor being studied. Expectations under random mating are often derived from discr...
journal_title：American journal of human genetics
pub_type： 杂志文章
doi：
更新日期：1983-09-01 00:00:00
abstract：:The distribution of HLA antigens in a sample of 124 Chagas serologically positive Chilean individuals was studied. The sample was subdivided according to the presence or absence of chagasic cardiomyopathy, in order to search for genetic differences associated with this pathological condition. The frequency of antigen ...
journal_title：American journal of human genetics
pub_type： 杂志文章
doi：
更新日期：1988-11-01 00:00:00
abstract：:A clinical description of an apparently classical case of type 1 GM1 gangliosidosis is presented. The patient was the first-born child of first cousins. She was diagnosed at 6 weeks and died at 6 months. beta-Galactosidase activity was deficient in cultured fibroblasts using [3H]GM1 ganglioside and [3H]ceramide-lactos...
journal_title：American journal of human genetics
pub_type： 杂志文章
doi：
更新日期：1979-11-01 00:00:00
abstract：:Molecular geneticists are developing the third-generation human genome map with single-nucleotide polymorphisms (SNPs), which can be assayed via chip-based microarrays. One use of these SNP markers is the ability to locate loci that may be responsible for complex traits, via linkage/linkage-disequilibrium analysis. In...
journal_title：American journal of human genetics
pub_type： 杂志文章
doi：10.1086/301909
更新日期：1998-07-01 00:00:00
abstract：:With the imminent availability of ultra-high-volume genotyping platforms (on the order of 100,000-1,000,000 genotypes per sample) at a manageable cost, there is growing interest in the possibility of conducting genomewide association studies for a variety of diseases but, so far, little consensus on methods to design ...
journal_title：American journal of human genetics
pub_type： 杂志文章,评审
doi：10.1086/432962
更新日期：2005-09-01 00:00:00
abstract：:Although psoriasis is strongly associated with certain human leukocyte antigens (HLAs), evidence for linkage to HLA markers has been limited. The objectives of this study were (1) to provide more definitive evidence for linkage of psoriasis to HLA markers in multiplex families; (2) to compare the major HLA risk allele...
journal_title：American journal of human genetics
pub_type： 杂志文章
doi：10.1086/301899
更新日期：1998-07-01 00:00:00
abstract：:An expansion of an unstable (CTG)n trinucleotide repeat in the 3' UTR of a gene encoding a putative serine/threonine protein kinase (DMPK) on human chromosome 19q13.3 has been shown to be specific for the myotonic dystrophy (DM) disease phenotype. In addition, a single haplotype composed of nine alleles within and fla...
journal_title：American journal of human genetics
pub_type： 杂志文章
doi：
更新日期：1995-05-01 00:00:00
abstract：:The still debated question of whether the expression of mental retardation in heterozygous carriers of the Martin-Bell syndrome is influenced by X inactivation has been investigated in a group of phase-known double heterozygotes for the FRA-X mutant and the G6PD Mediterranean variant. In these individuals, the number ...
journal_title：American journal of human genetics
pub_type： 杂志文章
doi：
更新日期：1990-04-01 00:00:00
abstract：:Studies have demonstrated that natural variation in the expression level of genes at baseline is extensive, and the determinants of this variation can be mapped by a genetic-linkage approach. In this study, we used lymphoblastoid cells to explore the variation in radiation-induced transcriptional changes. We found tha...
journal_title：American journal of human genetics
pub_type： 杂志文章
doi：10.1086/425221
更新日期：2004-11-01 00:00:00
abstract：:Primary hyperoxaluria type 1 (PH1) is a rare autosomal recessive disease caused by a deficiency of the liver-specific peroxisomal enzyme alanine:glyoxylate aminotransferase (AGT). Three unrelated PH1 patients, who possess a novel complex phenotype, are described. At the enzymological level, this phenotype is character...
journal_title：American journal of human genetics
pub_type： 杂志文章
doi：
更新日期：1993-08-01 00:00:00
abstract：:Linkage analysis of phenylketonurics has shown a strong association between the DNA haplotype at the phenylalanine hydroxylase (PAH) locus and phenylketonuria (PKU). Similarly, a genetic linkage between less severe forms of hyperphenylalaninemia (HPA) and the PAH locus has been suggested. In the present study we analy...
journal_title：American journal of human genetics
pub_type： 杂志文章
doi：
更新日期：1990-10-01 00:00:00
abstract：:Limb-girdle muscular dystrophies (LGMDs) are a group of neuromuscular diseases presenting great clinical heterogeneity. Mutations in CANP3, the gene encoding muscle-specific calpain, were used to identify this gene as the genetic site responsible for autosomal recessive LGMD type 2A (LGMD2A; MIM 253600). Analyses of t...
journal_title：American journal of human genetics
pub_type： 杂志文章
doi：
更新日期：1997-05-01 00:00:00
abstract：:Genome-wide association studies (GWASs) are commonly used for the mapping of genetic loci that influence complex traits. A problem that is often encountered in both population-based and family-based GWASs is that of identifying cryptic relatedness and population stratification because it is well known that failure to ...
journal_title：American journal of human genetics
pub_type： 杂志文章
doi：10.1016/j.ajhg.2012.05.024
更新日期：2012-07-13 00:00:00
abstract：:Living at high altitude is one of the most difficult challenges that humans had to cope with during their evolution. Whereas several genomic studies have revealed some of the genetic bases of adaptations in Tibetan, Andean, and Ethiopian populations, relatively little evidence of convergent evolution to altitude in di...
journal_title：American journal of human genetics
pub_type： 杂志文章
doi：10.1016/j.ajhg.2014.09.002
更新日期：2014-10-02 00:00:00
abstract：:Cone-rod dystrophy (CRD) and retinitis pigmentosa (RP) are clinically and genetically overlapping heterogeneous retinal dystrophies. By using homozygosity mapping in an individual with autosomal-recessive (ar) RP from a consanguineous family, we identified three sizeable homozygous regions, together encompassing 46 Mb...
journal_title：American journal of human genetics
pub_type： 杂志文章
doi：10.1016/j.ajhg.2011.11.015
更新日期：2012-01-13 00:00:00
abstract：:Despite the accelerated discovery of genes associated with syndromic traits, the majority of families affected by such conditions remain undiagnosed. Here, we employed whole-exome sequencing in two unrelated consanguineous kindreds with central nervous system (CNS), cardiac, renal, and digit abnormalities. We identifi...
journal_title：American journal of human genetics
pub_type： 杂志文章
doi：10.1016/j.ajhg.2017.02.007
更新日期：2017-04-06 00:00:00
